Hi McDog
I also have had my carbon woes with my Freak, fortunately used to well paid electrical engineer , so will try to apply my mind
Did the mounting bolt where the burning occurred have an earth lead connected to it. (I ask this as only one out of two mounting points showed some burning..that's odd..If it did, its heating the bolt up due to a bad connection at that joint..either the surface between mounting lug and ebox is dirty, or the crimped lug has failed inside the lead..that happens a lot..For it to generate that amount of heat would mean there is also another problem with the other earth lead which goes direct from battery negative terminal to starter motor mount...test it under high current load....same issue at the lugs or the strands are broken inside the sheathing somewhere where it flexes a lot whilst riding.
It did happen at just one bolt, but I really think it was current more than heat because it drained my 480cca lithium battery. That bolt isnt attached to anything more specific than the back of the ebox the same as the other two, but for some reason all the damage was at one bolt.
Another question.....did you see smoking at that mounting point when the engine was been cranked over, (e.g. 150 + Amps drawn from the battery) or was it happening without engine running at all. (and no water flowing at all)...maybe a bit more detail here please.
I actually never saw it smoking because a group of teenagers saw it and ignored it other than to tell me about it later. It was on a stand in a carport area just sitting.
Another angle .......the entire hull is carbon (highly conductive) and it has been earthed specifically at your ebox, (nowhere else in my mind) which in turn is earthed to the motor and battery.
So...as far as I am aware your battery positive leads are direct to solenoid and from there you send one to the bilge pump (via switch maybe ? or is the switch on the earth lead ) and probably another to Flame brain direct or via fuse. If no switch on positive lead to Bilge, the pump could be putting a voltage onto the hull where its mounted (i.e. faulty, wet inside) and current is making its way back to the battery via that mounting point and creating the heat.
Power to solenoid in box. Out to flame via fuse. Out to switch to bilge infused and then to bilge and bilge is grounded to common ground with the rest of the grounds.
Last thought....but left field completely....nothing to do with the battery circuits at all .....could be galvanic current flowing when you are riding (in salt water) and somehow this mounting point is the highest resistance in the whole current circuit therefore causing heat......I think you already replaced the aluminium tubes under the tray, which are destroyed by the galvanic effect of carbon/saltwater/aluminium, so now the pump nozzle or whole pump itself ( if not SS) becomes the preffered anode.....and the "problem " moves elsewhere....to the place where the hull meets its earth at the ebox.
I dont think its galvanic current as I was riding in fresh water that day. I never had aluminum tubing of any sort in this hull. It is all pex tubing with brass fittings and stainless crimps or pvc. The hull is not grounded at any other point.
my 2 cents